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Experimental Eye Research

Elsevier BV

All preprints, ranked by how well they match Experimental Eye Research's content profile, based on 32 papers previously published here. The average preprint has a 0.02% match score for this journal, so anything above that is already an above-average fit. Older preprints may already have been published elsewhere.

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Optimizing Tissue Clearing Methods for Improved Imaging of Whole-Mount Retinas

Mutschler, A.; Malechka, V. V.; Baranov, P.; Soucy, J. R.

2025-04-19 bioengineering 10.1101/2025.04.14.648787 medRxiv
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Gene and cell therapies are promising approaches for restoring vision in hereditary and advanced optic neuropathies. However, these therapeutic approaches must be accurately evaluated through a combination of methods, including advanced imaging, to reach the clinic. We present a whole-mount tissue-clearing methodology to improve imaging of donor neuron integration in the retina following cell transplantation in mice. Mouse retinas were processed using five different clearing methods, comparing tissue transparency, pigmentation, and immunohistochemical clarity. Among the tested methods, ScaleS consistently outperformed its peers, demonstrating a 46% increase in tissue transparency and an 89% increase in immunohistochemical clarity compared to controls. We developed a modified version of ScaleS, termed ScaleH, by adding polyvinyl alcohol to reduce fluorescence decay and enhance sample stability. ScaleH maintained fluorescence stability over extended periods (32% less decay) and proved compatible with immunolabeling and endogenous fluorescent reporters, enabling improved visualization of transplanted human stem cell-derived retinal neurons in the mouse retina. Moreover, ScaleH also improved optic nerve imaging, demonstrating the potential for broader neurobiological applications. Our clearing workflow supports robust, high-resolution imaging for evaluating the integration of transplanted cells in regenerative studies.

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Regenerative hallmarks of aging: Insights through the lens of Pleurodeles waltl

Tsissios, G.; Theodoroudis-Rapp, G.; Chen, W.; Sallese, A.; Smucker, B.; Ernst, L.; Chen, J.; Xu, Y.; Ratvasky, S.; Wang, H.; Del Rio-Tsonis, K.

2022-09-16 developmental biology 10.1101/2022.09.13.507508 medRxiv
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BackgroundAging and regeneration are heavily linked processes. While it is generally accepted that regenerative capacity declines with age, some vertebrates, such as newts, can bypass the deleterious effects of aging and successfully regenerate a lens throughout their lifetime. ResultsHere, we used Optical Coherence Tomography (OCT) to monitor the lens regeneration process of larvae, juvenile, and adult newts. While all three life stages were able to regenerate a lens through transdifferentiation of the dorsal iris pigment epithelial cells (iPECs), an age-related decline in the kinetics of the regeneration process was observed. Consistent with these findings, iPECs from older animals exhibited a delay in cell cycle re-entry. Furthermore, it was observed that clearance of the extracellular matrix (ECM) was delayed in older organisms. ConclusionsCollectively, our results suggest that although lens regeneration capacity does not decline throughout the lifespan of newts, the intrinsic and extrinsic cellular changes caused by aging alter the kinetics of this process. By understanding how aging affects lens regeneration in newts, we can gain important insights for restoring the age-related regeneration decline observed in most vertebrates.

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Microstructural determinants of lens stiffness in rat versus guinea pig lenses

Parreno, J.; Abera, K.; Aryal, S.; Forbes, K. E.; Fowler, V. M.

2021-02-16 cell biology 10.1101/2021.02.15.431302 medRxiv
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Proper ocular lens function requires lens biomechanical flexibility which is lost in presbyopia during aging. As increasing lens size has been shown previously to correlate with lens biomechanical stiffness in aging, we tested the hypothesis that whole lens size determines gross biomechanical stiffness. We used an allometric approach to evaluate this hypothesis by comparing lenses from three rodent species (mouse, rats and guinea pigs) of varying size. While rat lenses are larger and stiffer than mouse lenses, guinea pig lenses are even larger than rat lenses but are softer than the rat lens. This indicates that lens size is not a sole determinant of lens stiffness and disproves our hypothesis. Therefore, we investigated the scaling of lens microstructural features that could potentially explain the differences in biomechanical stiffness between rat and guinea pig lenses, including lens capsule thickness, epithelial cell area, fiber cell widths, suture organization, and nuclear size. Capsule thickness, epithelial cell area, and fiber cell widths scaled with lens size (i.e., greater in guinea pig lenses than rats), indicating that sizes of these features do not correlate with the stiffness of rat lenses, while suture organization was similar between rats and guinea pigs. However, we found that the hard rat lens nucleus occupies a greater fraction of the lens than the guinea pig lens nucleus, suggesting a role for nuclear size in determining whole lens stiffness. Therefore, while many features contribute to lens biomechanical properties, the size of the lens nucleus with respect to the size of the lens could be a major determinant of lens stiffness in rats versus guinea pigs.

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Single Cell Transcriptomics Identifies Distinct Choroid Cell Populations Involved in Visually Guided Eye Growth

Summers, J. A.; Jones, K. L.

2023-05-31 cell biology 10.1101/2023.05.30.542876 medRxiv
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Postnatal ocular growth is regulated by a vision-dependent mechanism, termed emmetropization, which acts to minimize refractive error through coordinated growth of the ocular tissues. Many studies suggest that the ocular choroid participates in the emmetropization process via the production of scleral growth regulators that control ocular elongation and refractive development. To elucidate the role of the choroid in emmetropization, we used single-cell RNA sequencing (scRNA-seq) to characterize the cell populations in the chick choroid and compare gene expression changes in these cell populations during conditions in which the eye is undergoing emmetropization. UMAP clustering analysis identified 24 distinct cell clusters in all chick choroids. 7 clusters were identified as fibroblast subpopulations; 5 clusters represented different populations of endothelial cells; 4 clusters were CD45+ macrophages, T cells and B cells; 3 clusters were Schwann cell subpopulations; and 2 clusters were identified as melanocytes. Additionally, single populations of RBCs, plasma cells and neuronal cells were identified. Significant changes in gene expression between control and treated choroids were identified in 17 cell clusters, representing 95% of total choroidal cells. The majority of significant gene expression changes were relatively small (< 2 fold). The highest changes in gene expression were identified in a rare cell population (0.11% - 0.49% of total choroidal cells). This cell population expressed high levels of neuron-specific genes as well as several opsin genes suggestive of a rare neuronal cell population that is potentially light sensitive. Our results, for the first time, provide a comprehensive profile of the major choroidal cell types and their gene expression changes during the process of emmetropization as well as insights into the canonical pathways and upstream regulators that coordinate postnatal ocular growth.

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Rhythmicity of photoreceptor outer segment phagocytosis differs between the cone subtypes in the larval zebrafish

Partinen, J.; Nevala, N.; Eramies, S.; Ihalainen, T. O.; Nymark, S.

2025-01-13 cell biology 10.1101/2025.01.10.632332 medRxiv
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Phagocytosis of retinal rod and cone outer segment (OS) tips by the retinal pigment epithelium (RPE) occurs daily to prevent accumulation of harmful compounds in the photoreceptors. Rhythmic bursts of phagocytosis, seen as increased levels of phagocytosed OS particles in the RPE, are known to appear once or twice a day depending on the animal species. However, differences in the rhythmicity of phagocytosis between distinct photoreceptor types are not well understood. Here, we show that phagocytosis of cone subtype OSs does not have identical rhythmic profiles in young zebrafish larvae. We investigated this by immunolabelling histological sections from the eyes of larvae that were collected at seven different time points throughout a 24 h circadian cycle. Internalized OS particles were then quantified from confocal images. The results revealed that OSs of all cone subtypes are phagocytosed continuously at some levels in young zebrafish. Interestingly, we observed a significant increase in the OS phagosome numbers from UV and blue cones at two time points, whereas green and red cones were phagocytosed more evenly throughout the day. We also investigated whether this rhythmicity is regulated by the external light by keeping the larvae in constant darkness before sample preparation. We found that complete darkness condition dampened the peaks in OS phagosome numbers from UV and blue cones indicating that the rhythmicity is primarily driven by the external light rather than the intrinsic circadian clocks in young larval zebrafish. Our findings provide new understanding on the rhythmicity of cone OS phagocytosis and its regulation.

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Fission of megamitochondria into multiple smaller well-defined mitochondria in the ageing zebrafish retina

Burgoyne, T.; Toms, M.; Way, C.; Tracey-White, D.; Futter, C.; Moosajee, M.

2021-12-10 cell biology 10.1101/2021.12.09.471958 medRxiv
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Mitochondria are essential adenosine triphosphate (ATP)-generating cellular organelles. In the retina, they are highly numerous in the photoreceptors and retinal pigment epithelium (RPE) due to their high energetic requirements. Fission and fusion of the mitochondria within these cells allow them to adapt to changing demands over the lifespan of the organism. Using transmission electron microscopy, we examined the mitochondrial ultrastructure of zebrafish photoreceptors and RPE from 5 days post fertilisation (dpf) through to late adulthood (3 years). Notably, mitochondria in the youngest animals were large and irregular shaped with a loose cristae architecture, but by 8 dpf they had reduced in size and expanded in number with more defined cristae. When investigating temporal gene expression of several mitochondrial-related markers, they indicated fission as the dominant mechanism contributing to these changes observed over time. This is likely to be due to continued mitochondrial stress resulting from the oxidative environment of the retina and prolonged light exposure. We have characterised retinal mitochondrial ageing in a key vertebrate model organism, that provides a basis for future studies of retinal diseases that are linked to mitochondrial dysfunction.

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Myopia alters the structural organization of the retinal astrocyte template, associated vasculature and ganglion layer thickness.

Lin, C. R.; Toychiev, A.; Slavi, N.; Srinivas, M.; Ablordeppey, R. K.; Benavente-Perez, A.

2022-02-24 developmental biology 10.1101/2022.02.22.481546 medRxiv
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PurposeTo describe the effect of myopic eye growth on the structure and distribution of astrocytes, vasculature and ganglion cell thickness, critical for inner retinal tissue homeostasis and survival. MethodsAstrocyte and capillary distribution, retinal nerve fiber (RNFL) and ganglion cell layer (GCL) thicknesses were assessed using immunochemistry and spectral domain optical coherence tomography on eleven retinas of juvenile common marmosets (Callithrix Jacchus), six of which were induced with lens-induced myopia (refraction, Rx: -7.01{+/-}1.8D). Five untreated age-matched juvenile marmoset retinas were used as controls (Rx: -0.74{+/-}0.4D). ResultsAs control marmoset eyes grew normally, there was an age-related increase in astrocyte numbers associated with RNFL thickening. Marmosets with induced myopia did not show this trend and, on the contrary, had reduced astrocyte numbers, increased positive GFAP immunopositive staining, thinner RNFL, lower peripheral capillary branching, and increased numbers of string vessels. ConclusionThe myopic changes in retinal astrocytes, vasculature, and ganglion cell layer thickness suggest a reorganization of the astrocyte and vascular templates during myopia development and progression. Whether these adaptations are beneficial or harmful to the retina remains to be investigated. Summary StatementThis article provides new information on how progressive myopia affects key elements of the retinal neurovascular unit.

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Effects of α-crystallin gene knockout on zebrafish lens development

Posner, M.; Murray, K. L.; Andrew, B.; Brdicka, S.; Butterbaugh-Roberts, A.; Franklin, K.; Hussen, A.; Kaye, T.; Kepp, E.; McDonald, M.; Snodgrass, T.; Zientek, K.; David, L.

2021-12-23 developmental biology 10.1101/2021.12.22.473921 medRxiv
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The -crystallin small heat shock proteins contribute to the transparency and refractive properties of the vertebrate eye lens and prevent the protein aggregation that would otherwise produce lens cataracts, the leading cause of human blindness. There are conflicting data in the literature as to what role the -crystallins may play in early lens development. In this study, we used CRISPR gene editing to produce zebrafish lines with null mutations for each of the three -crystallin genes (cryaa, cryaba and cryabb). The absence of normal protein was confirmed by mass spectrometry, and lens phenotypes were assessed with differential interference contrast microscopy and histology. Loss of A-crystallin produced a variety of lens defects with varying severity in larval lenses at 3 and 4 dpf but little substantial change in normal fiber cell denucleation. Loss of either Ba- or full-length Bb-crystallin produced no substantial lens defects. Mutation of each -crystallin gene did not alter the mRNA levels of the remaining two, suggesting a lack of genetic compensation. These data confirm a developmental role for A-crystallin in lens development, but the range of phenotype severity suggests that its loss simply increases the chance for defects and that the protein is not essential. Our finding that cryaba and cryabb mutants lack noticeable lens defects is congruent with insubstantial transcript levels in lens epithelial and fiber cells. Future experiments can explore the molecular consequences of cryaa mutation and causes of lens defects in this null mutant, as well as the roles of other genes in lens development and function.

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Analysis of mouse lens morphological and proteomic abnormalities following depletion of βB3-crystallin

Rayee, D.; Wilmarth, P. A.; VanSlyke, J. K.; Zientek, K.; Reddy, A. P.; Musil, L. S.; David, L. L.; Cvekl, A.

2024-12-31 developmental biology 10.1101/2024.12.30.630781 medRxiv
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Crystallin proteins serve as both essential structural and as well as protective components of the ocular lens and are required for the transparency and light refraction properties of the organ. The mouse lens crystallin proteome is represented by A-, B-, {beta}A1-, {beta}A2-, {beta}A3-, {beta}A4-, {beta}B1-, {beta}B2-, {beta}B3-, {gamma}A-, {gamma}B-, {gamma}C-, {gamma}D-, {gamma}E, {gamma}F-, {gamma}N-, and {gamma}S-crystallin proteins encoded by 16 genes. Their mutations are responsible for lens opacification and early onset cataract formation. While many cataract-causing missense and nonsense mutations are known for these proteins, including the human CRYBB3 gene, the mammalian loss-of function model of the Crybb3 gene remains to be established. Herein, we generated the first mouse model via deletion of the Crybb3 promoter that abolished expression of the {beta}B3-crystallin. Histological analysis of lens morphology using newborn {beta}B3-crystallin-deficient lenses revealed disrupted lens morphology with early-onset phenotypic variability. In-depth lens proteomics at four time points (newborn, 3-weeks, 6-weeks, and 3-months) showed both down- and up-regulation of various proteins, with the highest divergence from control mice observed in 3-months lenses. Apart from the {beta}B3-crystallin, another protein Smarcc1/Baf155 was down-regulated in all four samples. In addition, downregulation of Hspe1, Pdlim1, Ast/Got, Lsm7, Ddx23, and Acad11 was found in three time points. Finally, we show that the {beta}B3-crystallin promoter region, which contains multiple binding sites for the transcription factors AP-2, c-Jun, c-Maf, Etv5, and Pax6 is activated by FGF2 in primary lens cell culture experiments. Together, these studies establish the mouse Crybb3 loss-of-function model and its disrupted crystallin and non-crystallin proteomes.

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Multiparametric grading of glaucoma severity by histopathology can enable post-mortem substratification of disease state

Xiang, C.; Raghunathan, V.; Qiu, Y.; Mehta, M.; Grosskreutz, C. L.; Wilson, C. W.; Prasanna, G.

2024-05-21 pathology 10.1101/2024.05.18.594740 medRxiv
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Neurodegeneration in glaucoma patients is clinically identified through longitudinal assessment of structure-function changes, including intraocular pressure, cup-to-disc ratios from fundus images, and optical coherence tomography imaging of the retinal nerve fiber layer. Use of human post-mortem ocular tissue for basic research is rising in the glaucoma field, yet there are challenges in assessing disease stage and severity, since tissue donations with informed consent are often unaccompanied by detailed pre-mortem clinical information. Further, the interpretation of disease severity based solely on anatomical and morphological assessments by histology can be affected by differences in death-to-preservation time and tissue processing. These are difficult confounders that cannot be easily controlled. As pathogenesis and molecular mechanisms can vary depending on the stage and severity of glaucoma, there is a need for the field to maximize use of donated tissue to better understand the molecular mechanisms of glaucoma and develop new therapeutic hypotheses. Further, there is a lack of consensus around the molecular RNA and protein markers that can be used to classify glaucoma severity. Here, we describe a multiparametric grading system that combines structural measurements of the retinal nerve fiber layer with linear regression and principal component analyses of molecular markers of retinal ganglion cells and glia (RBPMS, NEFL, IBA1 and GFAP) to stratify post-mortem glaucoma eyes by the severity of disease. Our findings show that a quantitative grading approach can stratify post-mortem glaucoma samples with minimal clinical histories into at least three severity groups and suggest that this type of approach may be useful for researchers aiming to maximize insights derived from eye bank donor tissue.

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Comparison of Deep Learning Tools for Optic Nerve Axon Quantification Finds Limited Generalizability on Independent Validation

Chuter, B.; Emmert, N.; Kim, M. Y.; Dave, N.; Herrin, J.; Zhou, Z.; Wall, G.; Palmer, A.; Chen, H.; Hollingsworth, T. J.; Jablonski, M. M.

2026-03-13 bioengineering 10.64898/2026.03.11.710915 medRxiv
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PurposeMachine learning approaches for automated quantification of optic nerve histology have emerged as potential tools for objective assessment of axonal injury in experimental glaucoma models. However, the generalizability of these models to independent datasets remains unclear. Guided by a scoping review of the literature, this study performed independent validation testing of publicly available models on a novel rat optic nerve dataset to assess their generalizability. MethodsWe conducted a scoping review following PRISMA-ScR guidelines. PubMed, EMBASE, Scopus, and Cochrane CENTRAL were searched from 2000 through 2025. Two reviewers independently screened records and extracted data on model characteristics and performance metrics. Additionally, we performed independent validation of three models (AxoNet, AxonDeepSeg, AxoNet 2.0) on a novel rat optic nerve dataset comprising 57 images with 9,514 manually annotated axons. Because AxonDeep is not publicly available, we instead evaluated AxonDeepSeg, a separate publicly available deep learning-based tool that, while not previously applied to optic nerve tissue, is widely used for nerve fiber segmentation. ResultsFrom 2,036 records, four manuscripts describing three deep learning models met inclusion criteria. Published correlation coefficients between model predictions and reference counts ranged from 0.959 to 0.99. On independent validation, performance was reduced: AxoNet 2.0 achieved the highest correlation (r = 0.89), followed by AxonDeepSeg (r = 0.86) and AxoNet (r = 0.79). Segmentation quality metrics revealed high precision (>0.94) but low recall (0.18 to 0.27), with Dice coefficients of 0.29 to 0.40, substantially below published benchmarks of 0.81. ConclusionsDeep learning models for optic nerve histology demonstrate strong within-study performance but show meaningful performance decrements when applied to independent datasets. The observed generalizability gap (correlations 0.07 to 0.182 points below published values) demonstrates the need for standardized validation datasets and multi-center testing before widespread adoption of these tools.

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A Conserved Mechanism in Eye Optical Development: Lens Nucleus Centralization in Xenopus laevis

Garcia, K. A.; Tseng, K.; Vorontsova, I.

2025-11-11 developmental biology 10.1101/2025.11.09.687506 medRxiv
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Developing eye optics, determined by the lens and cornea, must coordinate with the axial length of growing eyes to focus light onto the retina to form an image. It was found that zebrafish (Danio rerio) lens nuclei are initially anteriorly localized in optical axes in larvae, then centralize at older stages. An anteriorly placed lens nucleus would increase lens power, thereby likely enabling a functional optical system in larvae, where eye axial length is short. To assess if alike mechanisms occur in other aquatic animals, we studied the clawed frog, Xenopus laevis, a fully aquatic species similarly relying on vision for survival at stages where eyes are small. We found the Xenopus tadpole lens nucleus also shifted from an anterior to a central location in the optical axis during the prometamorphosis period. Similarly, in eyes regenerated after embryonic ablation, tadpole lens nuclei are anteriorly localized then centralize before metamorphosis, recapitulating the same pattern as control developing eyes. Moreover, lens nuclei localization in optical axes in developing and regenerated Xenopus eyes show close correlations to axial eye length. Close correlation of these two parameters suggests lens nuclei centralization is required for a functional optical system by coordinating the focal length. Our findings suggest a conserved evolutionary mechanism for eye optical development in at least two aquatic species. Understanding key mechanisms regulating crosstalk between eye optics and eye axial length will aid in discovering mechanisms of optical development and future therapies to prevent or delay formation of refractive error when these two properties mismatch.

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Deletions of distant regulatory sequences upstream of zebrafish pitx2 result in a range of ocular phenotypes.

Weh, E.; Sorokina, E. A.; Hendee, K.; Gould, D.; Semina, E.

2019-09-18 genetics 10.1101/772426 medRxiv
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Development of the anterior segment of the vertebrate eye is a highly coordinated process. Genetic mutations in factors guiding this process result in Anterior Segment Dysgenesis (ASD), a spectrum of disorders affecting the iris, cornea, trabecular meshwork and/or other iridocorneal angle structures and associated with glaucoma. One of the first factors linked to ASD in humans was PITX2, a homeodomain containing transcription factor with a role in Axenfeld-Rieger syndrome (ARS). In addition to pathogenic alleles within the coding region of PITX2, deletions affecting the distant upstream region, but not PITX2 itself, have also been reported in ARS. Consistent with this, the distant upstream region was shown to contain multiple conserved elements (CE) with pitx2-related enhancer activity identified through studies in zebrafish. The two smallest human deletions reported to date encompass conserved elements 5-11 ({Delta}CE5-11) or 5-7 ({Delta}CE5-7). We previously reported the generation of{Delta} CE5-11 in zebrafish and we have now replicated the smallest deletion,{Delta} CE5-7, in the same model and studied the associated phenotype, expression, and DNA methylation profiles; we also performed further phenotypic examinations of the pitx2{Delta}CE5-11 fish. We show that the expression changes and phenotypes observed in the two lines are variable but that the severity generally correlates with the size of the deletion and the number of affected CEs; pitx2 promoter and a nearby region were hypermethylated in the pitx2{Delta}CE5-7 embryonic eyes. In addition, a subset of pitx2{Delta}CE5-11 animals were found to have a severe retinal phenotype suggesting that additional factors may modify the effects of this allele. These data provide further insight into functional sequences in the PITX2/pitx2 genomic region that coordinate PITX2/pitx2 expression during eye development and provide the basis for future studies into PITX2/pitx2 upstream regulators and modifiers.

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Identification of a Novel Alternatively Spliced CRYBA1 Transcript in Unilateral Childhood Cataract Associated with Persistent Fetal Vasculature

Sankaranarayanan, R.; Vasavada, A. R.; Agrawal, D.; Vasavada, S. A.; Vasavada, V. A.

2026-07-13 genetic and genomic medicine 10.64898/2026.07.08.26357271 medRxiv
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Purpose: To identify transcript-level variants in crystallin genes in paediatric patients with unilateral cataracts. Methods: Anterior capsulorhexis (n=12) from patients underwent surgical management of congenital unilateral cataracts was collected. Total RNA was isolated from lens epithelial cells, and complementary DNA (cDNA) was synthesized. Full-length RNA transcripts of 10 lens-specific crystallin genes were PCR-amplified and analysed via Sanger sequencing. Identified transcript variants were further validated using genomic DNA (gDNA) through Sanger sequencing. In addition, the full-length (~7,535 bp) CRYBA1 genomic region was sequenced using Oxford Nanopore Technology. Results: Aberrant low molecular weight (LMW) amplicons (~370 bp) of the CRYBA1 transcript were identified in three patients presented with unilateral cataract. Of 3 patients, 2 had persistent fetal vasculature (PFV) and 1 had pre-existing posterior capsular defect (PPCD). Sanger sequencing revealed a precise loss of exons 2 to 4 in the CRYBA1 RNA transcript. No coding, splice-site, or large deletion variants were detected in the genomic DNA of the patients or their parents. In silico analysis predicted two possible truncated proteins arising from these alternatively spliced transcripts: one comprising the first 11 amino acids of the N-terminal region with a loss of all Greek key motifs, and another comprising 90 amino acids encoded by exons 5 and 6, initiated from an alternative start codon in exon 5, and loss of Greek key motifs 1 & 2. Conclusion: The precise skipping of exons 2 to 4, consistent with canonical splicing signals (5-prime-GU...AG-3-prime), in the absence of genomic alterations, suggests the presence of alternatively spliced (AS) CRYBA1 transcripts in human lenses. This is the first report documenting AS-CRYBA1 transcripts in association with childhood cataracts with PFV and PPCD.

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Loss of GFAP cause retinal dysplasia and vision impairment

Sarusie, M. V. K.; Rönnbäck, C.; Jespersgaard, C.; Ali, Y.; Christensen, S. T.; Brondum-Nielsen, K.; Mollgard, K.; Rosenberg, T.; Larsen, L. A.; Gronskov, K.

2022-11-15 genetic and genomic medicine 10.1101/2022.11.09.22282105 medRxiv
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Diagnosis of genetic diseases has taken tremendous steps forward since the human genome project and technical advancements such as next generation sequencing. However, in the past years it has become evident that the classical "one gene - one phenotype" model is insufficient to encompass the intricacies of human genetics. Examples are emerging that variants in a gene can cause quite diverging phenotypes depending on the specific location in the gene or on the specific type of variant. In the era of precision medicine this is important knowledge, both when interpreting genomic data, but also when designing treatment strategies. Gain-of-function variants in GFAP leads to protein aggregation and is the cause of the severe neurodegenerative disorder Alexander Disease (AxD), while loss of GFAP function has been considered benign. Here, we report a loss-of-function variant in GFAP as the cause of optico-retinal dysplasia and vision impairment in a six-generation family. Whole genome sequencing analysis of family members with gliosis of the optic nerve head and visual impairment revealed a frameshift variant in GFAP (c.928dup, p.(Met310Asnfs*113)) segregating with disease. Analysis of human embryonic tissues revealed strong expression of GFAP in retinal neural progenitors. A zebrafish model verified that c.928dup does not result in extensive GFAP protein aggregation and zebrafish gfap loss-of-function mutants showed vision impairment and retinal dysplasia, characterized by a significant loss of Muller glia cells and photoreceptor cells. Our findings show how different mutational mechanisms can cause diverging phenotypes and reveal a novel function of GFAP in human eye development.

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Sialoglycoconjugate Profiling of Human Choroid, Retinal Pigment Epithelium, and Macular Degeneration Related Lesions

Navratil, E. M.; Wenzel, P. A.; Flamme-Wiese, M. J.; Miller, J. E. B.; Wiley, L. A.; Stone, E. M.; Tucker, B. A.; Mullins, R. F.

2025-04-23 cell biology 10.1101/2025.04.23.650306 medRxiv
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Age-related macular degeneration is a leading cause of central vision loss in the elderly. Early hallmarks of the disease include basal laminar deposit and choriocapillaris degeneration. The location and composition of sialoglycoconjugates in healthy and diseased choroid and disease-related lesions have not been thoroughly examined. This study utilized lectins to examine sialoglycoconjugates in human tissue, specifically Sambucus nigra/Elderberry Bark Lectin (EBL) and Maackia amurensis lectin II (MAL-II), to examine -2,6 and -2,3 sialic acids, respectively. EBL and MAL-II both label the choroid and basal laminar deposit, with slightly different patterns. Whereas MAL-II predominantly labels the choriocapillaris endothelium, EBL also labels Bruchs membrane and extracellular domains surrounding the vasculature (intercapillary pillars). EBL labeling overlaps with the distribution of complement factor H to a greater extent than MAL-II. After treatment with neuraminidase to remove terminal sialic acids, a battery of lectins was applied to sections of choroids. Lectins that recognize {beta}-galactose, N-acetyllactosamine, galactose ({beta}-1,3) N-acetylgalactosamine, and - or {beta}-N-acetylgalactosamine showed increased reactivity, including increased labeling of glycans in basal laminar deposits. This study provides insight into the location and partial identities of sialoglycoconjugates in the human choroid, with possible implications for the pathogenesis of macular degeneration.

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Evidence of Presence and Activation of the two Cell Cycle Kinases Nek6 and Nek7 in the ciliated Neuroretina

Janisch, K. M.; Kasanuki, J. M.; Davis, R. J.; Tsang, S. H.

2020-03-29 biochemistry 10.1101/2020.03.27.012724 medRxiv
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The serine/threonine NIMA kinases are widely found in eukaryotes. They are cell-cycle kinases that are associated with centrosomes and spindle apparatus and cilia. In cilia, NIMA kinases are reported to play a role in cilia length maintenance and deflagelation. Here we focus on the two Nek homologs, Nek6 and Nek7, and their potential role in retina. We report for the first-time expression of nek6 and nek7 mRNA and protein in retinal tissue. In particular, we detect localisation of these kinases to photoreceptors outer segments. Moreover, we are able to show a light-dependent phosphorylation of the activation loop (serine 206) of Nek6/7 in rod outer segments, suggesting activation of these kinases is downstream of the phototransduction pathway. Indeed, we demonstrate that Nek6/7 phosphorylation in the retina is dependent on Grk1 function. Furthermore, Nek6/7 phosphorylation can be stimulated in the brain by opiate drugs, suggesting that activation of Nek6/7 lies downstream of G protein coupled receptors activation, in general. Nek6/7 may couple photoreception with outer segment biogenesis through phosphorylation of downstream substrates, which may affect the microtubules of the axoneme.

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Retinal gene and pathway modulation by benzathine penicillin: A potential link to Extensive Macular Atrophy with Pseudodrusen (EMAP) and neurodegeneration.

Shinsato, R. N.; Herai, R. H.

2025-09-17 genetics 10.1101/2025.09.15.676285 medRxiv
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Extensive Macular Atrophy with Pseudodrusen (EMAP) is a rare and rapidly progressive retinal disease marked by central vision loss, chorioretinal atrophy, and pseudodrusen, primarily affecting middle-aged individuals. Recent studies have identified a statistically significant association between long-term use of benzathine penicillin (BP) and the onset of EMAP. However, the molecular mechanisms underlying this relationship remain unclear. In this study, we performed an integrative in silico analysis to explore the genes modulated by BP that are expressed in ocular tissues and involved in retinal metabolic pathways. Using public databases (PubChem, GTEx, HPA, EYEDB), we identified 52 BP-responsive genes, with six (CD4, CRP, IL6, IL1R1, TAC1, TNF) directly modulated by BP and expressed in the retina. These genes are implicated in inflammation, immune response, and retinal homeostasis. Expression data show strong presence in eye and brain tissues, and several are associated with age-related macular degeneration (AMD). Network analysis revealed gene-gene and protein-protein interactions, highlighting a shared pathophysiological axis. Notably, IL6 and TNF are involved in oxidative stress, endoplasmic reticulum stress, and chronic inflammation--hallmarks of both EMAP and atrophic AMD. Our findings suggest that BP may induce EMAP by dysregulating retinal genes involved in neurodegeneration, providing new insights into drug safety and retinal disease mechanisms.

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Cannabinoid signaling promotes the reprogramming of Muller glia into proliferating progenitor cells.

Campbell, W.; Blum, S.; Reske, A.; Hoang, T.; Blackshaw, S.; Fischer, A.

2021-03-25 molecular biology 10.1101/2021.03.25.436969 medRxiv
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Endocannabinoids (eCB) are lipid-based neurotransmitters that are known to influence synaptic function in the visual system. eCBs are also known to suppress neuroinflammation in different pathological states. However, nothing is known about the roles of the eCB system during reprogramming of Muller glia (MG) into proliferating progenitor-like cells in the retina. Accordingly, we used the chick and mouse model to characterize expression patterns of eCB-related genes and applied pharmacological agents to examine how the eCB system impacts glial reactivity and the capacity of MG to become Muller glia-derived progenitor cells (MGPCs). We probed single cell RNA-seq libraries to identify eCB-related genes and identify cells with dynamic patterns of expression in damaged retinas. MG and inner retinal neurons expressed the eCB receptor CNR1, as well as enzymes involved in eCB metabolism. In the chick, intraocular injections of 2-Arachidonoylglycerol (2-AG) and Anandamide (AEA) potentiated the formation of MGPCs. Consistent with these findings, CNR1-agonists and MGLL-inhibitor promoted reprogramming, whereas CNR1-antagonist and inhibitors of eCB synthesis suppressed reprogramming. Surprisingly, retinal microglia were largely unaffected by increases or decreases in eCB signaling in both chick and mouse models. However, eCB-signaling suppressed the activation of NFkB-reporter in MG in damaged mouse retinas. We conclude that the eCB system in the retina influences the reactivity of MG and is important for regulating glial reactivity and the reprogramming of MG into proliferating MGPCs, but not for regulating the reactivity of immune cells in the retina. Main PointsMuller glia express CNR1 receptor and endocannabinoid synthesis genes. Endocannabinoids after retinal damage promote the formation of Muller glia derived progenitor cells in chick. Endocannabinoids reduce NFkB activity in mouse Muller glia.

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Epigallocatechin Gallate (EGCG) as a Protective Agent Against Enzymatic Stromal Degradation in Caprine and Ovine Corneas: Towards Novel Therapeutics for Keratoconus

Khan, M. U. A.; Ahmad, S. T.; Nisar, S.; Khan, R. N.; Khan, F. F.

2026-02-02 pathology 10.64898/2026.01.30.697846 medRxiv
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PurposeKeratoconus (KC) is a progressive corneal ectatic disorder marked by stromal thinning, enzymatic degradation, and oxidative stress. Conventional corneal collagen cross-linking (CXL) therapy poses risks. Epigallocatechin gallate (EGCG), a catechin found in green tea, has been shown to cross-link collagen, inhibit proteases, and modulate inflammation, suggesting its potential as an alternative therapy for KC. This study aimed to (1) evaluate the protective effects of EGCG against collagenase-mediated stromal degradation in caprine and ovine corneas and (2) investigate the use of caprine and ovine cornea as viable ex vivo models for corneal ectasia research. MethodsGoat (n=4) and sheep (n=8) corneoscleral buttons were cultured in an air-liquid interface (ALI). Tissue viability was monitored by transparency grading and histology. The corneal ectasia environment was induced by collagenase type I digestion. An EGCG-rich extract was utilized for the treatments. ResultsGoat and sheep corneas remained intact for 7 days in MEM-based medium, though transparency decreased, with edema (whitening) by Day 7. Histology confirmed stromal loosening and reduced keratocyte cell density but preserved architecture sufficient for enzymatic digestion. EGCG pre-treatment and post-treatment exposure were associated with greater resistance to enzymatic digestion, with greater stromal preservation of quadrants in the EGCG pre-treated quadrant than in PBS pre-treated controls. ConclusionsThis study provides proof of concept that EGCG extract confers protection against enzymatic degradation in goat and sheep corneas, highlighting its potential as a protective agent for corneal ectatic disorders like Keratoconus. Additionally, goat and sheep corneas can represent practical and ethical ex vivo models for short-term ocular research. Future work should focus on cytotoxicity, biomechanical validation, optimized culture conditions, and in vivo studies.